Generated Code

function [VOI, STATES, ALGEBRAIC, CONSTANTS] = mainFunction()
    % This is the "main function".  In Matlab, things work best if you rename this function to match the filename.
   [VOI, STATES, ALGEBRAIC, CONSTANTS] = solveModel();
end

function [algebraicVariableCount] = getAlgebraicVariableCount() 
    % Used later when setting a global variable with the number of algebraic variables.
    % Note: This is not the "main method".  
    algebraicVariableCount =0;
end
% There are a total of 3 entries in each of the rate and state variable arrays.
% There are a total of 11 entries in the constant variable array.
%

function [VOI, STATES, ALGEBRAIC, CONSTANTS] = solveModel()
    % Create ALGEBRAIC of correct size
    global algebraicVariableCount;  algebraicVariableCount = getAlgebraicVariableCount();
    % Initialise constants and state variables
    [INIT_STATES, CONSTANTS] = initConsts;

    % Set timespan to solve over 
    tspan = [0, 10];

    % Set numerical accuracy options for ODE solver
    options = odeset('RelTol', 1e-06, 'AbsTol', 1e-06, 'MaxStep', 1);

    % Solve model with ODE solver
    [VOI, STATES] = ode15s(@(VOI, STATES)computeRates(VOI, STATES, CONSTANTS), tspan, INIT_STATES, options);

    % Compute algebraic variables
    [RATES, ALGEBRAIC] = computeRates(VOI, STATES, CONSTANTS);
    ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI);

    % Plot state variables against variable of integration
    [LEGEND_STATES, LEGEND_ALGEBRAIC, LEGEND_VOI, LEGEND_CONSTANTS] = createLegends();
    figure();
    plot(VOI, STATES);
    xlabel(LEGEND_VOI);
    l = legend(LEGEND_STATES);
    set(l,'Interpreter','none');
end

function [LEGEND_STATES, LEGEND_ALGEBRAIC, LEGEND_VOI, LEGEND_CONSTANTS] = createLegends()
    LEGEND_STATES = ''; LEGEND_ALGEBRAIC = ''; LEGEND_VOI = ''; LEGEND_CONSTANTS = '';
    LEGEND_VOI = strpad('time in component environment (minute)');
    LEGEND_STATES(:,1) = strpad('X1 in component X1 (ng_ml)');
    LEGEND_CONSTANTS(:,1) = strpad('a0 in component X1 (ng_ml_min)');
    LEGEND_CONSTANTS(:,2) = strpad('a1 in component X1 (ng_ml_min)');
    LEGEND_CONSTANTS(:,3) = strpad('a2 in component X1 (dl_microg)');
    LEGEND_CONSTANTS(:,4) = strpad('b1 in component X1 (first_order_rate_constant)');
    LEGEND_STATES(:,2) = strpad('X3 in component X3 (microg_dl)');
    LEGEND_STATES(:,3) = strpad('X2 in component X2 (pg_ml)');
    LEGEND_CONSTANTS(:,5) = strpad('a3 in component X2 (pg_ml_min)');
    LEGEND_CONSTANTS(:,6) = strpad('a4 in component X2 (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,7) = strpad('a5 in component X2 (dl_microg)');
    LEGEND_CONSTANTS(:,8) = strpad('b2 in component X2 (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,9) = strpad('a6 in component X3 (microg_dl_min)');
    LEGEND_CONSTANTS(:,10) = strpad('a7 in component X3 (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,11) = strpad('b3 in component X3 (first_order_rate_constant)');
    LEGEND_RATES(:,1) = strpad('d/dt X1 in component X1 (ng_ml)');
    LEGEND_RATES(:,3) = strpad('d/dt X2 in component X2 (pg_ml)');
    LEGEND_RATES(:,2) = strpad('d/dt X3 in component X3 (microg_dl)');
    LEGEND_STATES  = LEGEND_STATES';
    LEGEND_ALGEBRAIC = LEGEND_ALGEBRAIC';
    LEGEND_RATES = LEGEND_RATES';
    LEGEND_CONSTANTS = LEGEND_CONSTANTS';
end

function [STATES, CONSTANTS] = initConsts()
    VOI = 0; CONSTANTS = []; STATES = []; ALGEBRAIC = [];
    STATES(:,1) = 10.0;
    CONSTANTS(:,1) = 0.0014;
    CONSTANTS(:,2) = 0.000517;
    CONSTANTS(:,3) = 0.0164;
    CONSTANTS(:,4) = 0.0598;
    STATES(:,2) = 0.0;
    STATES(:,3) = 0.0;
    CONSTANTS(:,5) = 1.38;
    CONSTANTS(:,6) = 0.60;
    CONSTANTS(:,7) = 0.00498;
    CONSTANTS(:,8) = 0.053;
    CONSTANTS(:,9) = 0.0084;
    CONSTANTS(:,10) = 0.0081;
    CONSTANTS(:,11) = 0.0138;
    if (isempty(STATES)), warning('Initial values for states not set');, end
end

function [RATES, ALGEBRAIC] = computeRates(VOI, STATES, CONSTANTS)
    global algebraicVariableCount;
    statesSize = size(STATES);
    statesColumnCount = statesSize(2);
    if ( statesColumnCount == 1)
        STATES = STATES';
        ALGEBRAIC = zeros(1, algebraicVariableCount);
        utilOnes = 1;
    else
        statesRowCount = statesSize(1);
        ALGEBRAIC = zeros(statesRowCount, algebraicVariableCount);
        RATES = zeros(statesRowCount, statesColumnCount);
        utilOnes = ones(statesRowCount, 1);
    end
    RATES(:,1) = (CONSTANTS(:,1)+CONSTANTS(:,2)./(1.00000+ CONSTANTS(:,3).*STATES(:,2))) -  CONSTANTS(:,4).*STATES(:,1);
    RATES(:,3) = (CONSTANTS(:,5)+ CONSTANTS(:,6).*STATES(:,1))./(1.00000+ CONSTANTS(:,7).*STATES(:,2)) -  CONSTANTS(:,8).*STATES(:,3);
    RATES(:,2) = (CONSTANTS(:,9)+ CONSTANTS(:,10).*STATES(:,3)) -  CONSTANTS(:,11).*STATES(:,2);
   RATES = RATES';
end

% Calculate algebraic variables
function ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI)
    statesSize = size(STATES);
    statesColumnCount = statesSize(2);
    if ( statesColumnCount == 1)
        STATES = STATES';
        utilOnes = 1;
    else
        statesRowCount = statesSize(1);
        utilOnes = ones(statesRowCount, 1);
    end
end

% Pad out or shorten strings to a set length
function strout = strpad(strin)
    req_length = 160;
    insize = size(strin,2);
    if insize > req_length
        strout = strin(1:req_length);
    else
        strout = [strin, blanks(req_length - insize)];
    end
end